Here we present datasets underlying the results of the study examining patterns of structural and functional community-level change in a range of well-studied marine ecosystems with documented histories of bioinvasion. For the purpose of the study, the authors identified six regions with extensive bay-scale datasets on native and non-indigenous benthic species assemblages, allowing paired comparisons in time (years to decades; retrospective datasets) or space (high vs. low proximity to hotspots of NIS introductions within a region; cross-sectional datasets) representing differences in bioinvasion pressure (Table 1). These sites were: 1) coastal waters of British Columbia, Canada (BC); 2) San Francisco Bay, USA (SF); 3) Ilha Grande Bay, Brazil (BR); 4) North-Eastern Baltic Sea, Estonia (BS); 5) estuaries of New South Wales, Australia (AU) and 6) Waitematā Harbour, New Zealand (NZ). These six regions are generally at mid- to higher-latitudes, with one low-latitude site (BR). The study sites encompassed surveys of benthic communities: fouling assemblages (BC and AU), subtidal reefs (BR and BS), and soft-sediment benthos (SF, BS, and NZ). Three data files are provided for each study region and include: benthic community data (XX_species.csv) binary (0/1) biological trait information compiled for all species in the dataset (XX_traits.csv) additional explanatory variables considered for each study region - bioinvasion pressure and spatial variables (XX_env.csv) For detailed information on datasets and methods description please refer to the original manuscript by Zaiko et al.